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Conserved domains on  [gi|66474957|gb|AAY47008|]
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methyltransferase/corrinoid binding protein, partial [Hyphomicrobium sp. TW28]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
B12-binding_like super family cl00293
B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 ...
 133-254 4.21e-50

B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins. Not all members of this family contain the conserved binding motif.


The actual alignment was detected with superfamily member cd02070:

Pssm-ID: 469709 [Multi-domain]  Cd Length: 201  Bit Score: 162.79  E-value: 4.21e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474957 133 LVEAIMEYDGDKAIEWVKKGLERGMTAQDIVFDGLSLGMKVVGDMYERNERFVTDMLKAAKTMDKAMPILTPLLEQAGGD 212
Cdd:cd02070   1 LADAIVDGDEEETVELVKKALEAGIDPQDIIEEGLAPGMDIVGDKYEEGEIFVPELLMAADAMKAGLDLLKPLLGKSKSA 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 66474957 213 ggPTGTVVVGLVRGNTQDIGKNLVCLMLKANGFKVIDLGKNV 254
Cdd:cd02070  81 --KKGKVVIGTVEGDIHDIGKNLVATMLEANGFEVIDLGRDV 120
URO-D_CIMS_like super family cl00464
The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen ...
 1-78 2.04e-32

The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine synthases. Despite their sequence similarities, members of this family have clearly different functions. Uroporphyrinogen decarboxylase (URO-D) decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, an important branching point of the tetrapyrrole biosynthetic pathway. The methyltransferases represented here are important for ability of methanogenic organisms to use other compounds than carbon dioxide for reduction to methane, and methionine synthases transfer a methyl group from a folate cofactor to L-homocysteine in a reaction requiring zinc.


The actual alignment was detected with superfamily member TIGR01463:

Pssm-ID: 469779  Cd Length: 336  Bit Score: 121.08  E-value: 2.04e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 66474957     1 MDHAKRAIGGQISLMGTLSPFSTLMHGsttdVANEVKKLAAEVGYNGGLIVMPGCDIDWTIPDENLKAMIETCASIKY 78
Cdd:TIGR01463 263 MAHGKRVIGGRASLVGNLSPPFTLLNG----TPEKIKAEAKEVLEGGIDILAPGCGIAPMTPLENLKAMVEACKEIYY 336
 
Name Accession Description Interval E-value
corrinoid_protein_B12-BD cd02070
B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins ...
 133-254 4.21e-50

B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.


Pssm-ID: 239021 [Multi-domain]  Cd Length: 201  Bit Score: 162.79  E-value: 4.21e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474957 133 LVEAIMEYDGDKAIEWVKKGLERGMTAQDIVFDGLSLGMKVVGDMYERNERFVTDMLKAAKTMDKAMPILTPLLEQAGGD 212
Cdd:cd02070   1 LADAIVDGDEEETVELVKKALEAGIDPQDIIEEGLAPGMDIVGDKYEEGEIFVPELLMAADAMKAGLDLLKPLLGKSKSA 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 66474957 213 ggPTGTVVVGLVRGNTQDIGKNLVCLMLKANGFKVIDLGKNV 254
Cdd:cd02070  81 --KKGKVVIGTVEGDIHDIGKNLVATMLEANGFEVIDLGRDV 120
MtbC1 COG5012
Methanogenic corrinoid protein MtbC1 [Energy production and conversion];
121-254 4.40e-40

Methanogenic corrinoid protein MtbC1 [Energy production and conversion];


Pssm-ID: 444036 [Multi-domain]  Cd Length: 219  Bit Score: 137.72  E-value: 4.40e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474957 121 KELTPQQEVNEKLVEAIMEYDGDKAIEWVKKGLERGMTAQDIVFDGLSLGMKVVGDMYERNERFVTDMLKAAKTMDKAMP 200
Cdd:COG5012   2 LTRPYGEELLESLADAVLEGDEDEALELVAEALAAGMDPEEIILDGLAPGMREVGELWEEGEIFVPEEHLAAAAMKAGLE 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 66474957 201 ILTPLLEQAGGDGgptGTVVVGLVRGNTQDIGKNLVCLMLKANGFKVIDLGKNV 254
Cdd:COG5012  82 ILKPLLAEEGGRK---GKVVIGTVEGDLHDIGKNIVADMLRAAGFEVIDLGADV 132
mtaA_cmuA TIGR01463
methyltransferase, MtaA/CmuA family; This subfamily is closely related to, yet is distinct ...
 1-78 2.04e-32

methyltransferase, MtaA/CmuA family; This subfamily is closely related to, yet is distinct from, uroporphyrinogen decarboxylase (EC 4.1.1.37). It includes two isozymes from Methanosarcina barkeri of methylcobalamin--coenzyme M methyltransferase. It also includes a chloromethane utilization protein, CmuA, which transfers the methyl group of chloromethane to a corrinoid protein.


Pssm-ID: 273639  Cd Length: 336  Bit Score: 121.08  E-value: 2.04e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 66474957     1 MDHAKRAIGGQISLMGTLSPFSTLMHGsttdVANEVKKLAAEVGYNGGLIVMPGCDIDWTIPDENLKAMIETCASIKY 78
Cdd:TIGR01463 263 MAHGKRVIGGRASLVGNLSPPFTLLNG----TPEKIKAEAKEVLEGGIDILAPGCGIAPMTPLENLKAMVEACKEIYY 336
pyl_corrinoid TIGR02370
methyltransferase cognate corrinoid proteins, Methanosarcina family; This model describes a ...
 132-254 3.32e-28

methyltransferase cognate corrinoid proteins, Methanosarcina family; This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.


Pssm-ID: 131423 [Multi-domain]  Cd Length: 197  Bit Score: 106.42  E-value: 3.32e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474957   132 KLVEAIMEYDGDKAIEWVKKGLERGMTAQDIVFDGLSLGMKVVGDMYERNERFVTDMLKAAKTMDKAMPILTPLLEQAGG 211
Cdd:TIGR02370   1 KLAKAIFEGEEDDVVEGAQKALDAGIDPIELIEKGLMAGMGVVGKLFEDGELFLPHVMMSADAMLAGIKVLTPEMEKAVE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 66474957   212 DGGpTGTVVVGLVRGNTQDIGKNLVCLMLKANGFKVIDLGKNV 254
Cdd:TIGR02370  81 TEV-LGKVVCGVAEGDVHDIGKNIVVTMLRANGFDVIDLGRDV 122
B12-binding_2 smart01018
B12 binding domain; Cobalamin-dependent methionine synthase is a large modular protein that ...
 127-210 7.34e-20

B12 binding domain; Cobalamin-dependent methionine synthase is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain. The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases.


Pssm-ID: 198086 [Multi-domain]  Cd Length: 84  Bit Score: 80.98  E-value: 7.34e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474957    127 QEVNEKLVEAIMEYDGDKAIEWVKKGLERGMTAQDIVFDGLSLGMKVVGDMYERNERFVTDMLKAAKTMDKAMPILTPLL 206
Cdd:smart01018   1 MPLLERLAEAIVDGDEEGVEELVEEALAEGVDPLEIINEGLIPGMNVVGDLFEAGEYFLPQVLMSAEAMKAAVAILKPLL 80


                   ....
gi 66474957    207 EQAG 210
Cdd:smart01018  81 EKEK 84
URO-D_like cd03465
The URO-D _like protein superfamily includes bacterial and eukaryotic uroporphyrinogen ...
 1-75 1.36e-18

The URO-D _like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases. Uroporphyrinogen decarboxylase (URO-D) decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, an important branching point of the tetrapyrrole biosynthetic pathway. The methyltransferases represented here are important for ability of methanogenic organisms to use other compounds than carbon dioxide for reduction to methane.


Pssm-ID: 239548  Cd Length: 330  Bit Score: 83.15  E-value: 1.36e-18
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 66474957   1 MDHAKRAIGGQISLMGTLSPFSTLMHGSTTDVANEVKKLAAEVGYN-GGLIVMPGCDIDWTIPDENLKAMIETCAS 75
Cdd:cd03465 255 LAEAKKKVGDKACLMGNLDPIDVLLNGSPEEIKEEVKELLEKLLKGgGGYILSSGCEIPPDTPIENIKAMIDAVRE 330
HemE COG0407
Uroporphyrinogen-III decarboxylase HemE [Coenzyme transport and metabolism]; ...
 1-73 2.79e-18

Uroporphyrinogen-III decarboxylase HemE [Coenzyme transport and metabolism]; Uroporphyrinogen-III decarboxylase HemE is part of the Pathway/BioSystem: Heme biosynthesis


Pssm-ID: 440176 [Multi-domain]  Cd Length: 336  Bit Score: 82.58  E-value: 2.79e-18
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 66474957   1 MDHAKRAIGGQISLMGTLSPFSTLMHGSTTDVANEVKKLAAEVGYNGGLIVMPGCDIDWTIPDENLKAMIETC 73
Cdd:COG0407 260 LAEAKERLGDKVALQGNLDPALLLLNGTPEEVEAEVKRILDAGGGGPGHIFNLGHGIPPDTPPENVKALVEAV 332
B12-binding_2 pfam02607
B12 binding domain; This B12 binding domain is found in methionine synthase EC:2.1.1.13, and ...
 133-202 8.38e-15

B12 binding domain; This B12 binding domain is found in methionine synthase EC:2.1.1.13, and other shorter proteins that bind to B12. This domain is always found to the N-terminus of pfam02310. The structure of this domain is known, it is a 4 helix bundle. Many of the conserved residues in this domain are involved in B12 binding, such as those in the MXXVG motif.


Pssm-ID: 460617 [Multi-domain]  Cd Length: 68  Bit Score: 67.11  E-value: 8.38e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474957   133 LVEAIMEYDGDKAIEWVKKGLErgMTAQDIVFDGLSLGMKVVGDMYERNERFVTDMLKAAKTMDKAMPIL 202
Cdd:pfam02607   1 LLEALLEGDEEAAEELLEEALE--IDPEEIIEDLLIPGMDEVGELWEAGEIFVPQEHLAAEAMKAALAVL 68
metH PRK09490
B12-dependent methionine synthase; Provisional
 170-251 1.36e-13

B12-dependent methionine synthase; Provisional


Pssm-ID: 236539 [Multi-domain]  Cd Length: 1229  Bit Score: 70.21  E-value: 1.36e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474957   170 GMKVVGDMYERNERFVTDMLKAAKTMDKAMPILTPLLE---QAGGDGGPTGTVVVGLVRGNTQDIGKNLVCLMLKANGFK 246
Cdd:PRK09490  702 GMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEakkEGGTDRKSNGKILMATVKGDVHDIGKNIVGVVLQCNNYE 781


                  ....*
gi 66474957   247 VIDLG 251
Cdd:PRK09490  782 VIDLG 786
URO-D pfam01208
Uroporphyrinogen decarboxylase (URO-D);
4-73 6.74e-11

Uroporphyrinogen decarboxylase (URO-D);


Pssm-ID: 460112 [Multi-domain]  Cd Length: 341  Bit Score: 61.45  E-value: 6.74e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 66474957     4 AKRAIGGQISLMGTLSPFstLMHGSTTDVANEVKK-LAAEVGYNGGLIVMPGCDIDWTIPDENLKAMIETC 73
Cdd:pfam01208 270 AARRVGDRVALQGNLDPA--VLLGSPEEIRKEVKEiLEKGIDGPKGYILNLGHGIPPGTPPENVKALVEAV 338
PRK06252 PRK06252
methylcobalamin:coenzyme M methyltransferase; Validated
 4-79 7.82e-09

methylcobalamin:coenzyme M methyltransferase; Validated


Pssm-ID: 235753  Cd Length: 339  Bit Score: 55.27  E-value: 7.82e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 66474957    4 AKRAIGGQISLMGTLSPFSTLMHGSTTDVANEVKK-LAAEVGyngglIVMPGCDIDWTIPDENLKAMIETCASIKYP 79
Cdd:PRK06252 268 AKENVGDRAALIGNVSTSFTLLNGTPEKVKAEAKKcLEDGVD-----ILAPGCGIAPKTPLENIKAMVEARKEYYAE 339
 
Name Accession Description Interval E-value
corrinoid_protein_B12-BD cd02070
B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins ...
 133-254 4.21e-50

B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases.


Pssm-ID: 239021 [Multi-domain]  Cd Length: 201  Bit Score: 162.79  E-value: 4.21e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474957 133 LVEAIMEYDGDKAIEWVKKGLERGMTAQDIVFDGLSLGMKVVGDMYERNERFVTDMLKAAKTMDKAMPILTPLLEQAGGD 212
Cdd:cd02070   1 LADAIVDGDEEETVELVKKALEAGIDPQDIIEEGLAPGMDIVGDKYEEGEIFVPELLMAADAMKAGLDLLKPLLGKSKSA 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 66474957 213 ggPTGTVVVGLVRGNTQDIGKNLVCLMLKANGFKVIDLGKNV 254
Cdd:cd02070  81 --KKGKVVIGTVEGDIHDIGKNLVATMLEANGFEVIDLGRDV 120
MtbC1 COG5012
Methanogenic corrinoid protein MtbC1 [Energy production and conversion];
121-254 4.40e-40

Methanogenic corrinoid protein MtbC1 [Energy production and conversion];


Pssm-ID: 444036 [Multi-domain]  Cd Length: 219  Bit Score: 137.72  E-value: 4.40e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474957 121 KELTPQQEVNEKLVEAIMEYDGDKAIEWVKKGLERGMTAQDIVFDGLSLGMKVVGDMYERNERFVTDMLKAAKTMDKAMP 200
Cdd:COG5012   2 LTRPYGEELLESLADAVLEGDEDEALELVAEALAAGMDPEEIILDGLAPGMREVGELWEEGEIFVPEEHLAAAAMKAGLE 81

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 66474957 201 ILTPLLEQAGGDGgptGTVVVGLVRGNTQDIGKNLVCLMLKANGFKVIDLGKNV 254
Cdd:COG5012  82 ILKPLLAEEGGRK---GKVVIGTVEGDLHDIGKNIVADMLRAAGFEVIDLGADV 132
mtaA_cmuA TIGR01463
methyltransferase, MtaA/CmuA family; This subfamily is closely related to, yet is distinct ...
 1-78 2.04e-32

methyltransferase, MtaA/CmuA family; This subfamily is closely related to, yet is distinct from, uroporphyrinogen decarboxylase (EC 4.1.1.37). It includes two isozymes from Methanosarcina barkeri of methylcobalamin--coenzyme M methyltransferase. It also includes a chloromethane utilization protein, CmuA, which transfers the methyl group of chloromethane to a corrinoid protein.


Pssm-ID: 273639  Cd Length: 336  Bit Score: 121.08  E-value: 2.04e-32
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 66474957     1 MDHAKRAIGGQISLMGTLSPFSTLMHGsttdVANEVKKLAAEVGYNGGLIVMPGCDIDWTIPDENLKAMIETCASIKY 78
Cdd:TIGR01463 263 MAHGKRVIGGRASLVGNLSPPFTLLNG----TPEKIKAEAKEVLEGGIDILAPGCGIAPMTPLENLKAMVEACKEIYY 336
MetH2 COG1410
Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]; ...
 108-254 5.69e-30

Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]; Methionine synthase I, cobalamin-binding domain is part of the Pathway/BioSystem: Methionine biosynthesis


Pssm-ID: 441020 [Multi-domain]  Cd Length: 1141  Bit Score: 118.13  E-value: 5.69e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474957  108 AGDTDVAEAKTHHKELTPQqEVNEKLVEAIMEYDGDKAIEWVKKGLERGMTAQDIVFDGLSLGMKVVGDMYERNERFVTD 187
Cdd:COG1410  607 FEGVKGAKAKKADLEWREL-PVEERLKHAIVKGIKEGIEEDTEEALAEGARPLEIINGPLMPGMNVVGDLFGAGKMFLPQ 685

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 66474957  188 MLKAAKTMDKAMPILTPLLEQAGGDGGPTGTVVVGLVRGNTQDIGKNLVCLMLKANGFKVIDLGKNV 254
Cdd:COG1410  686 VLKSAEVMKAAVAYLEPFMEKEKGESSSKGKIVLATVKGDVHDIGKNIVGVVLENNGYEVIDLGVMV 752
pyl_corrinoid TIGR02370
methyltransferase cognate corrinoid proteins, Methanosarcina family; This model describes a ...
 132-254 3.32e-28

methyltransferase cognate corrinoid proteins, Methanosarcina family; This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere.


Pssm-ID: 131423 [Multi-domain]  Cd Length: 197  Bit Score: 106.42  E-value: 3.32e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474957   132 KLVEAIMEYDGDKAIEWVKKGLERGMTAQDIVFDGLSLGMKVVGDMYERNERFVTDMLKAAKTMDKAMPILTPLLEQAGG 211
Cdd:TIGR02370   1 KLAKAIFEGEEDDVVEGAQKALDAGIDPIELIEKGLMAGMGVVGKLFEDGELFLPHVMMSADAMLAGIKVLTPEMEKAVE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 66474957   212 DGGpTGTVVVGLVRGNTQDIGKNLVCLMLKANGFKVIDLGKNV 254
Cdd:TIGR02370  81 TEV-LGKVVCGVAEGDVHDIGKNIVVTMLRANGFDVIDLGRDV 122
methionine_synthase_B12_BD cd02069
B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as ...
 129-254 4.23e-21

B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).


Pssm-ID: 239020 [Multi-domain]  Cd Length: 213  Bit Score: 88.09  E-value: 4.23e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474957 129 VNEKLVEAIMEYDGDKAIEWVKKGLERGMTAQDIVFDGLSLGMKVVGDMYERNERFVTDMLKAAKTMDKAMPILTPLLEQ 208
Cdd:cd02069   1 VEERLKHALVKGIRDGIEEDTEEARQQYARPLEIINGPLMDGMKVVGDLFGAGKMFLPQVLKSARVMKAAVAYLEPYMEK 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 66474957 209 AGGDGGPTGTVVVGLVRGNTQDIGKNLVCLMLKANGFKVIDLGKNV 254
Cdd:cd02069  81 EKGENSSKGKIVLATVKGDVHDIGKNLVGVILSNNGYEVIDLGVMV 126
B12-binding_2 smart01018
B12 binding domain; Cobalamin-dependent methionine synthase is a large modular protein that ...
 127-210 7.34e-20

B12 binding domain; Cobalamin-dependent methionine synthase is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain. The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases.


Pssm-ID: 198086 [Multi-domain]  Cd Length: 84  Bit Score: 80.98  E-value: 7.34e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474957    127 QEVNEKLVEAIMEYDGDKAIEWVKKGLERGMTAQDIVFDGLSLGMKVVGDMYERNERFVTDMLKAAKTMDKAMPILTPLL 206
Cdd:smart01018   1 MPLLERLAEAIVDGDEEGVEELVEEALAEGVDPLEIINEGLIPGMNVVGDLFEAGEYFLPQVLMSAEAMKAAVAILKPLL 80


                   ....
gi 66474957    207 EQAG 210
Cdd:smart01018  81 EKEK 84
URO-D_like cd03465
The URO-D _like protein superfamily includes bacterial and eukaryotic uroporphyrinogen ...
 1-75 1.36e-18

The URO-D _like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases. Uroporphyrinogen decarboxylase (URO-D) decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, an important branching point of the tetrapyrrole biosynthetic pathway. The methyltransferases represented here are important for ability of methanogenic organisms to use other compounds than carbon dioxide for reduction to methane.


Pssm-ID: 239548  Cd Length: 330  Bit Score: 83.15  E-value: 1.36e-18
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 66474957   1 MDHAKRAIGGQISLMGTLSPFSTLMHGSTTDVANEVKKLAAEVGYN-GGLIVMPGCDIDWTIPDENLKAMIETCAS 75
Cdd:cd03465 255 LAEAKKKVGDKACLMGNLDPIDVLLNGSPEEIKEEVKELLEKLLKGgGGYILSSGCEIPPDTPIENIKAMIDAVRE 330
HemE COG0407
Uroporphyrinogen-III decarboxylase HemE [Coenzyme transport and metabolism]; ...
 1-73 2.79e-18

Uroporphyrinogen-III decarboxylase HemE [Coenzyme transport and metabolism]; Uroporphyrinogen-III decarboxylase HemE is part of the Pathway/BioSystem: Heme biosynthesis


Pssm-ID: 440176 [Multi-domain]  Cd Length: 336  Bit Score: 82.58  E-value: 2.79e-18
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 66474957   1 MDHAKRAIGGQISLMGTLSPFSTLMHGSTTDVANEVKKLAAEVGYNGGLIVMPGCDIDWTIPDENLKAMIETC 73
Cdd:COG0407 260 LAEAKERLGDKVALQGNLDPALLLLNGTPEEVEAEVKRILDAGGGGPGHIFNLGHGIPPDTPPENVKALVEAV 332
B12-binding_2 pfam02607
B12 binding domain; This B12 binding domain is found in methionine synthase EC:2.1.1.13, and ...
 133-202 8.38e-15

B12 binding domain; This B12 binding domain is found in methionine synthase EC:2.1.1.13, and other shorter proteins that bind to B12. This domain is always found to the N-terminus of pfam02310. The structure of this domain is known, it is a 4 helix bundle. Many of the conserved residues in this domain are involved in B12 binding, such as those in the MXXVG motif.


Pssm-ID: 460617 [Multi-domain]  Cd Length: 68  Bit Score: 67.11  E-value: 8.38e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474957   133 LVEAIMEYDGDKAIEWVKKGLErgMTAQDIVFDGLSLGMKVVGDMYERNERFVTDMLKAAKTMDKAMPIL 202
Cdd:pfam02607   1 LLEALLEGDEEAAEELLEEALE--IDPEEIIEDLLIPGMDEVGELWEAGEIFVPQEHLAAEAMKAALAVL 68
metH PRK09490
B12-dependent methionine synthase; Provisional
 170-251 1.36e-13

B12-dependent methionine synthase; Provisional


Pssm-ID: 236539 [Multi-domain]  Cd Length: 1229  Bit Score: 70.21  E-value: 1.36e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 66474957   170 GMKVVGDMYERNERFVTDMLKAAKTMDKAMPILTPLLE---QAGGDGGPTGTVVVGLVRGNTQDIGKNLVCLMLKANGFK 246
Cdd:PRK09490  702 GMNVVGDLFGEGKMFLPQVVKSARVMKQAVAYLEPFIEakkEGGTDRKSNGKILMATVKGDVHDIGKNIVGVVLQCNNYE 781


                  ....*
gi 66474957   247 VIDLG 251
Cdd:PRK09490  782 VIDLG 786
Mta_CmuA_like cd03307
MtaA_CmuA_like family. MtaA/CmuA, also MtsA, or methyltransferase 2 (MT2) MT2-A and MT2-M ...
 4-75 2.53e-11

MtaA_CmuA_like family. MtaA/CmuA, also MtsA, or methyltransferase 2 (MT2) MT2-A and MT2-M isozymes, are methylcobamide:Coenzyme M methyltransferases, which play a role in metabolic pathways of methane formation from various substrates, such as methylated amines and methanol. Coenzyme M, 2-mercaptoethylsulfonate or CoM, is methylated during methanogenesis in a reaction catalyzed by three proteins. A methyltransferase methylates the corrinoid cofactor, which is bound to a second polypeptide, a corrinoid protein. The methylated corrinoid protein then serves as a substrate for MT2-A and related enzymes, which methylate CoM.


Pssm-ID: 239423  Cd Length: 326  Bit Score: 62.69  E-value: 2.53e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 66474957   4 AKRAIGGQISLMGTLSPFSTLMHGSTTDVANEVKK-LAAEVGyngglIVMPGCDIDWTIPDENLKAMIETCAS 75
Cdd:cd03307 259 AKEIVGGRAALIGNVSPSQTLLNGTPEDVKAEARKcLEDGVD-----ILAPGCGIAPRTPLANLKAMVEARKE 326
URO-D pfam01208
Uroporphyrinogen decarboxylase (URO-D);
4-73 6.74e-11

Uroporphyrinogen decarboxylase (URO-D);


Pssm-ID: 460112 [Multi-domain]  Cd Length: 341  Bit Score: 61.45  E-value: 6.74e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 66474957     4 AKRAIGGQISLMGTLSPFstLMHGSTTDVANEVKK-LAAEVGYNGGLIVMPGCDIDWTIPDENLKAMIETC 73
Cdd:pfam01208 270 AARRVGDRVALQGNLDPA--VLLGSPEEIRKEVKEiLEKGIDGPKGYILNLGHGIPPGTPPENVKALVEAV 338
B12-binding cd02067
B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 ...
 218-254 2.80e-10

B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.


Pssm-ID: 239018 [Multi-domain]  Cd Length: 119  Bit Score: 56.36  E-value: 2.80e-10
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 66474957 218 TVVVGLVRGNTQDIGKNLVCLMLKANGFKVIDLGKNV 254
Cdd:cd02067   1 KVVIATVGGDGHDIGKNIVARALRDAGFEVIDLGVDV 37
PRK06252 PRK06252
methylcobalamin:coenzyme M methyltransferase; Validated
 4-79 7.82e-09

methylcobalamin:coenzyme M methyltransferase; Validated


Pssm-ID: 235753  Cd Length: 339  Bit Score: 55.27  E-value: 7.82e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 66474957    4 AKRAIGGQISLMGTLSPFSTLMHGSTTDVANEVKK-LAAEVGyngglIVMPGCDIDWTIPDENLKAMIETCASIKYP 79
Cdd:PRK06252 268 AKENVGDRAALIGNVSTSFTLLNGTPEKVKAEAKKcLEDGVD-----ILAPGCGIAPKTPLENIKAMVEARKEYYAE 339
B12-binding_like cd02065
B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 ...
 218-254 6.46e-06

B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins. Not all members of this family contain the conserved binding motif.


Pssm-ID: 239016 [Multi-domain]  Cd Length: 125  Bit Score: 44.30  E-value: 6.46e-06
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 66474957 218 TVVVGLVRGNTQDIGKNLVCLMLKANGFKVIDLGKNV 254
Cdd:cd02065   1 KVLGATVGGDVHDIGKNIVAIALRDNGFEVIDLGVDV 37
B12-binding pfam02310
B12 binding domain; This domain binds to B12 (adenosylcobamide), it is found in several ...
 217-254 3.24e-04

B12 binding domain; This domain binds to B12 (adenosylcobamide), it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, which is important for B12 binding.


Pssm-ID: 426713 [Multi-domain]  Cd Length: 121  Bit Score: 39.62  E-value: 3.24e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 66474957   217 GTVVVGLVRGNTQDIGKNLVCLMLKANGFKVIDLGKNV 254
Cdd:pfam02310   1 GKVVVATVGGDLHPLGLNYVAAALRAAGFEVIILGANV 38
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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